44ccfacbe3a3d4b300f80d48651c77837a4b571e
galt
  Tue Apr 26 11:12:02 2022 -0700
SQL INJECTION Prevention Version 2 - this improves our methods by making subclauses of SQL that get passed around be both easy and correct to use. The way that was achieved was by getting rid of the obscure and not well used functions sqlSafefFrag and sqlDyStringPrintfFrag and replacing them with the plain versions of those functions, since these are not needed anymore. The new version checks for NOSQLINJ in unquoted %-s which is used to include SQL clauses, and will give an error the NOSQLINJ clause is not present, and this will automatically require the correct behavior by developers. sqlDyStringPrint is a very useful function, however because it was not enforced, users could use various other dyString functions and they operated without any awareness or checking for SQL correct use. Now those dyString functions are prohibited and it will produce an error if you try to use a dyString function on a SQL string, which is simply detected by the presence of the NOSQLINJ prefix.

diff --git src/hg/perf/hgTracksRandom.c src/hg/perf/hgTracksRandom.c
index f427373..bf5715a 100644
--- src/hg/perf/hgTracksRandom.c
+++ src/hg/perf/hgTracksRandom.c
@@ -1,218 +1,220 @@
 /* hgTracksRandom - For a given organism, view hgTracks (default tracks) in random position.
                     Record display time. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "chromInfo.h"
 #include "dystring.h"
 #include "hash.h"
 #include "hdb.h"
 #include "htmlPage.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "options.h"
 #include "portable.h"
 #include <signal.h>
 
 
 static char *database = NULL;
 static boolean quiet = FALSE;
 static struct hash *chromHash = NULL;
 
 /* command line option specifications */
 static struct optionSpec optionSpecs[] = {
     {"machines", OPTION_STRING},
     {"quiet", OPTION_BOOLEAN},
     {NULL, 0}
 };
 
 struct machine 
     {
     struct machine *next;
     char *name;
     };
 
 struct machine *machineList;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgTracksRandom - Time default view for random position of default genome\n"
   "usage:\n"
   "  hgTracksRandom <machines> [options]\n"
   "options:\n"
   "   <machines> is a file listing the machines to test\n"
   "   -quiet - only outputs the timing numbers, no machine names\n");
 }
 
 /* this is the second instance of this, it needs to find its program
  * name to become a generic function in the libs
  */
 /* if this Apoptosis function becomes more popular, it can go into the libs
  * there is a similar function in hg/lib/web.c cgiApoptosis()
  */
 static unsigned long expireSeconds = 0;
 /* to avoid long running processes on the RR */
 static void selfApoptosis(int status)
 /* signal handler for SIGALRM expiration */
 {
 if (expireSeconds > 0)
     {
     /* want to see this error message in the apache error_log also */
     fprintf(stderr, "hgTracksRandom selfApoptosis: %lu seconds\n", expireSeconds);
     /* this message may show up somewhere */
     errAbort("procedures have exceeded timeout: %lu seconds, function has ended.\n", expireSeconds);
     }
 exit(0);
 }
 
 void getMachines(char *filename)
 /* Read in list of machines to use. */
 {
 struct lineFile *lf = lineFileOpen(filename, TRUE);
 char *line;
 int lineSize;
 struct machine *machine;
 
 while (lineFileNext(lf, &line, &lineSize))
     {
     AllocVar(machine);
     // is this equivalent to slAddHead?
     machine->name = line;
     machine->next = machineList;
     machineList = machine;
     }
 /* could reverse order here */
 }
 
 /* Copied from hgLoadWiggle. */
 static struct hash *loadAllChromInfo()
 /* Load up all chromosome infos. */
 {
 struct chromInfo *el;
 struct sqlConnection *conn = sqlConnect(database);
 struct sqlResult *sr = NULL;
 struct hash *ret;
 char **row;
 
 ret = newHash(0);
 
-sr = sqlGetResult(conn, NOSQLINJ "select * from chromInfo");
+char query[1024];
+sqlSafef(query, sizeof query, "select * from chromInfo");
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = chromInfoLoad(row);
     verbose(4, "Add hash %s value %u (%#lx)\n", el->chrom, el->size, (unsigned long)&el->size);
     hashAdd(ret, el->chrom, (void *)(& el->size));
     }
 sqlFreeResult(&sr);
 sqlDisconnect(&conn);
 return ret;
 }
 
 /* also copied from hgLoadWiggle. */
 static unsigned getChromSize(char *chrom)
 /* Return size of chrom.  */
 {
 struct hashEl *el = hashLookup(chromHash,chrom);
 
 if (el == NULL)
     errAbort("Couldn't find size of chrom %s", chrom);
 return *(unsigned *)el->val;
 }   
 
 
 
 long hgTracksRandom(char *url)
 /* hgTracksRandom - Time default view for random position. */
 /* The URL can include position. */
 {
 long startTime, endTime;
 struct htmlPage *rootPage;
 
 startTime = clock1000();
 rootPage = htmlPageGet(url);
 endTime = clock1000();
 
 htmlPageValidateOrAbort(rootPage);
 if (rootPage->status->status != 200)
    errAbort("%s returned with status code %d", url, rootPage->status->status);
 
 return endTime - startTime;
 }
 
 int getStartPos(int chromSize, int windowSize)
 /* return a random start position */
 {
 if (windowSize >= chromSize)
     return 0;
 return rand() % (chromSize - windowSize);
 }
 
 int main(int argc, char *argv[])
 {
 struct dyString *dy = NULL;
 int startPos = 1;
 char *chrom = "chr1";
 int chromSize = 0;
 int windowSize = 100000;
 struct machine *machinePos;
 time_t now;
 char testTime[100];
 char testDate[100];
 long elapsedTime = 0;
 
 optionInit(&argc, argv, optionSpecs);
 
 expireSeconds = 300;	/* 5 minutes */
 (void) signal(SIGALRM, selfApoptosis);
 (void) alarm(expireSeconds);	/* CGI timeout */
 
 quiet = optionExists("quiet");
 now = time(NULL);
 strftime(testTime, 100, "%H:%M", localtime(&now));
 strftime(testDate, 100, "%B %d, %Y", localtime(&now));
 if (!quiet)
     printf("%s %s\n", testDate, testTime);
 
 if (argc != 2)
     usage();
 
 srand( (unsigned) time(NULL) );
 
 database = hDefaultDbForGenome(NULL); // default human db
 
 chromHash = loadAllChromInfo();
 chromSize = getChromSize(chrom);
 startPos = getStartPos(chromSize, windowSize);
 if (! quiet)
     printf("%s %s:%d-%d\n\n", database, chrom, startPos, startPos + windowSize);
 
 getMachines(argv[1]);
 
 for (machinePos = machineList; machinePos != NULL; machinePos = machinePos->next)
     {
-    dy = newDyString(256);
+    dy = dyStringNew(256);
     dyStringPrintf(dy, "%s/cgi-bin/hgTracks?db=%s&position=%s:%d-%d", machinePos->name, 
                    database, chrom, startPos, startPos + windowSize);
     elapsedTime = hgTracksRandom(dy->string);
     if (quiet)
 	{
 	printf("%ld\n", elapsedTime);
 	}
     else
 	{
 	if (elapsedTime > 5000)
 	    printf("%s %ld <---\n", machinePos->name, elapsedTime);
 	else
 	    printf("%s %ld\n", machinePos->name, elapsedTime);
 	}
     }
 if (! quiet)
     printf("----------------------------------\n");
 
 /* free machine list */
 return 0;
 }